Tue Oct 11 08:21:16 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 08:21:16 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3137 !!! WARNING: GLU 161 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5519979 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 55.14000 99.56001 ymin,ymax (A): -3.141000 54.77300 zmin,zma (A): 38.27400 102.7670 x,y,z range (A): 44.42000 57.91400 64.49300 scale (grids/A): 0.5519979 object centre (A): 77.35001 25.81600 70.52050 number of atom coordinates read : 3137 total number of charged atoms : 3000 net assigned charge : -4.271964 assigned positive charge : 466.5019 centred at (gu) : 90.63223 91.36105 93.27068 assigned negative charge : -470.7750 centred at (gu) : 90.65844 91.36590 93.32526 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5847 nv = 96 ne = 84 npr = 67405 no. pairs analyzed = 67405 no. exposed pairs = 3683 no. arc points = 25936 no. surface atoms = 1242 nbur = 1895 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 200 mr = 3074 m= 0 mr = 7 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2664 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7865 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5330845E-11 -1.7752882E-09 midg,1,midg; midg,igrid,midg -1.9579284E-10 -4.8879678E-10 1,midg,midg; igrid,midg,midg -7.4686778E-11 -6.2712524E-10 gauss-seidel spectral radius is 0.9830766 estimated iterations to convergence 63 setup time was (sec) 0.5400000 now iterating at: 08:21:17 rms-change max change #iterations 8.0299862E-02 15.37214 at 10iterations 5.6987344E-03 0.9205379 at 20iterations 5.8585644E-04 9.6706778E-02 at 30iterations 1.1951360E-04 2.2751331E-02 at 40iterations 3.0698287E-05 5.8693886E-03 at 50iterations finished qdiffx linear iterations at : 08:21:20 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 3.0698287E-05 5.8693886E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 08:21:21 3.353u 0.205s 0:04.24 83.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 08:21:21 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3137 !!! WARNING: GLU 161 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.655994 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 55.14000 99.56001 ymin,ymax (A): -3.141000 54.77300 zmin,zma (A): 38.27400 102.7670 x,y,z range (A): 44.42000 57.91400 64.49300 scale (grids/A): 1.655994 object centre (A): 77.35001 25.81600 70.52050 number of atom coordinates read : 3137 total number of charged atoms : 3000 net assigned charge : -4.271964 assigned positive charge : 466.5019 centred at (gu) : 91.89606 94.08236 99.81125 assigned negative charge : -470.7750 centred at (gu) : 91.97495 94.09734 99.97526 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 64413 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25936 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19402 mr = 43839 m= 1994 mr = 13475 m= 51 mr = 978 m= 0 mr = 3 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1194 time to turn everything in is 0.4700000 number of dielectric boundary points 27565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 318 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 23003 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5519979 object centre at (A) : 77.35001 25.81600 70.52050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6578233E-02 -6.6394391E-03 midg,1,midg; midg,igrid,midg -2.4279635E-03 9.8460140E-03 1,midg,midg; igrid,midg,midg -2.5917629E-03 -1.0748253E-02 gauss-seidel spectral radius is 0.9982303 estimated iterations to convergence 189 setup time was (sec) 0.7500000 now iterating at: 08:21:21 rms-change max change #iterations 3.480608 144.8321 at 10iterations 1.463697 51.70002 at 20iterations 0.6195497 22.42970 at 30iterations 0.2606281 9.472565 at 40iterations 0.1100907 4.219049 at 50iterations 4.6441000E-02 1.682353 at 60iterations 1.9733168E-02 0.6916631 at 70iterations 8.3604585E-03 0.2743104 at 80iterations 3.5674321E-03 0.1239920 at 90iterations 1.5475549E-03 5.9545517E-02 at 100iterations 6.9381366E-04 2.5892258E-02 at 110iterations 3.2640435E-04 1.3207436E-02 at 120iterations finished qdiffx linear iterations at : 08:21:28 total time elapsed so far: 7.130000 # loops : 120 mean,max change (kT/e) : 3.2640435E-04 1.3207436E-02 energy calculations done at 7.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.310000 DelPhi exited at 08:21:28 7.315u 0.214s 0:07.86 95.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 08:21:28 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3137 !!! WARNING: GLU 161 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.483991 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 55.14000 99.56001 ymin,ymax (A): -3.141000 54.77300 zmin,zma (A): 38.27400 102.7670 x,y,z range (A): 44.42000 57.91400 64.49300 scale (grids/A): 2.483991 object centre (A): 77.35001 25.81600 70.52050 number of atom coordinates read : 3137 total number of charged atoms : 3000 net assigned charge : -4.271964 assigned positive charge : 466.5019 centred at (gu) : 92.84396 96.12330 104.7167 assigned negative charge : -470.7750 centred at (gu) : 92.96225 96.14592 104.9626 start vw surface at 0.1600000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 149966 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25936 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67470 mr = 107599 m= 19299 mr = 53532 m= 3118 mr = 14597 m= 189 mr = 2021 m= 3 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 4232 time to turn everything in is 1.120000 number of dielectric boundary points 62202 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 23975 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.655994 object centre at (A) : 77.35001 25.81600 70.52050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3847608 -0.2343556 midg,1,midg; midg,igrid,midg 2.9996471E-03 0.3478148 1,midg,midg; igrid,midg,midg -2.8874954E-02 -0.1478109 gauss-seidel spectral radius is 0.9991525 estimated iterations to convergence 271 setup time was (sec) 1.430000 now iterating at: 08:21:30 rms-change max change #iterations 8.894442 361.8519 at 10iterations 4.995284 124.0331 at 20iterations 2.799084 74.67181 at 30iterations 1.560785 33.77667 at 40iterations 0.8694305 17.95618 at 50iterations 0.4833449 10.10772 at 60iterations 0.2676138 5.237131 at 70iterations 0.1483635 3.402058 at 80iterations 8.2281619E-02 1.719518 at 90iterations 4.5435179E-02 0.9515247 at 100iterations 2.5254123E-02 0.5191517 at 110iterations 1.3954318E-02 0.2965962 at 120iterations 7.7486630E-03 0.1599264 at 130iterations 4.3130508E-03 9.4308376E-02 at 140iterations 2.4176941E-03 5.3991795E-02 at 150iterations 1.3684247E-03 3.5986900E-02 at 160iterations 7.9032121E-04 1.7580986E-02 at 170iterations 4.6960174E-04 1.1851311E-02 at 180iterations finished qdiffx linear iterations at : 08:21:40 total time elapsed so far: 11.58000 # loops : 180 mean,max change (kT/e) : 4.6960174E-04 1.1851311E-02 energy calculations done at 11.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.75000 DelPhi exited at 08:21:41 11.756u 0.235s 0:12.40 96.6% 0+0k 0+0io 0pf+0w